As far as I have been able to determine, the Convert Format tool always saves the converted file with just two channels. I believe that it just pulls the front left and right channels, and does not down-mix 5.1 (for example) to stereo.
See the third paragraph in my post here:
http://yabb.jriver.com/interact/index.php?topic=92612.msg637577#msg637577I am pretty sure that one of the developers, I think Hendrik, confirmed that for me at one time. But I can't find the post again. From memory, Hendrik also said it would be good to improve the formats available that the converter supports, but it was a can of worms in that the number of format combinations from source to target was enormous, so it would be difficult to work out which conversions to implement. I also think there was some issue around writing the AC-3 format. Possibly a licencing issue? But then I can get the converter to write AC-3, but only in stereo.
I started doing some more testing a little while ago, converting from JTV to TS to see if I could get 5.1 output from 5.1 AC-3 source. It was depressing. The best I got was stereo AC-3. Often I get stereo AAC.
Therefore, to answer your question OverTheAir, yes, the Convert Format tool only supports output of two channels. I would love someone to prove me wrong, but I won't hold my breath.
If you haven't, also read this thread:
http://yabb.jriver.com/interact/index.php?topic=92387.0Specifically, given the constraints of the Convert Format tool, and the benefits of using the JTV format, I have decided not to use the TS format. Yaobing explains the main benefit of the JTV format here:
http://yabb.jriver.com/interact/index.php?topic=92387.msg636416#msg636416